amplab snap issues - Githubissues

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

https://www.microsoft.com/en-us/research/project/snap/

Apache License 2.0

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issues

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Allocate overflow entries with BigAlloc

#19 mateiz closed 9 years ago
1
Always turn on -c for index build

#18 mateiz closed 12 years ago
1
TLEN should be 0 for paired reads where the ends map cross-chromosome

#17 bolosky closed 12 years ago
1
Fails to write SAM file

#16 antunderwood closed 3 years ago
5
-F flag doesn't apply filter to unalignable reads

#15 bolosky closed 12 years ago
1
CIGAR string option to use "M" instead of "=" or "X" for compatibility

#14 rnpandya closed 12 years ago
1
SAM reader complains about SAM file with sequences not matching reference

#13 mateiz closed 3 years ago
0
Option to write aligned and unaligned reads to different files

#12 mateiz closed 12 years ago
1
Paired input files with differing read lengths

#11 rnpandya closed 9 years ago
4
Single-file output on Linux

#10 rnpandya closed 12 years ago
1
Sort output by alignment location

#9 rnpandya closed 12 years ago
1
BAM file output

#8 rnpandya closed 9 years ago
1
Add NM edit distance field to SAM output

#7 rnpandya closed 12 years ago
1
Improve hash table sizing for small genomes

#6 rnpandya closed 12 years ago
1
Misalignment in RNA-seq data

#5 rnpandya closed 12 years ago
2
Should be able to index human reference in 64Gb RAM

#4 rnpandya closed 9 years ago
1
Read groups in SAM file header

#3 rnpandya closed 9 years ago
3
SAM output of mate pairs when only one is mapped

#2 rnpandya closed 12 years ago
2
Insertions at end of reads

#1 rnpandya closed 9 years ago
1